4MXN

Crystal structure of a putative glycosyl hydrolase (PARMER_00599) from Parabacteroides merdae ATCC 43184 at 1.95 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4MXN/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides merdae ATCC 43184
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-26 Released: 2013-10-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.213 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Crystal structure of a hypothetical protein (PARMER_00599) from Parabacteroides merdae ATCC 43184 at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.6 kDa 
• Atom Count: 7,261 
• Modelled Residue Count: 898 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	247	Parabacteroides merdae ATCC 43184	Mutation(s): 0  Gene Names: PARMER_00599

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.213 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M34MXN

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.65	α = 90.89
b = 62.43	β = 118.34
c = 67.96	γ = 100.63

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary